Officials with the Greater Toronto Airports Authority (GTAA) said there are problems with the computer program that airlines use to register passengers at check-in.
"IT providers are on scene working to rectify the situation as quickly as possible, but it is expected that check-in will continue to be slow throughout the morning," the GTAA said in a statement.
"We apologize for the inconvenience that this is causing to passengers as they check in at the airport this morning."
Airline workers are checking travellers in manually, a more time-consuming process, the organization said.
As a result of the delays, the GTAA says passengers should plan for it to take longer to go through the check-in process, and is encouraging flyers use the airport's web check-in service before arriving at the transport hub.
There's no word yet on when the problems will be fixed.
Saturday's delays come less than a week after severe weather, including a deep freeze that afflicted much of central Canada and Northern United States, resulted in the cancellation of hundreds of flights at Pearson.